Sun Oct 9 14:04:34 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 14:04:34 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2373 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6890144 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 21.36800 70.38500 ymin,ymax (A): -1.748000 49.92000 zmin,zma (A): -5.585000 37.30200 x,y,z range (A): 49.01700 51.66800 42.88700 scale (grids/A): 0.6890144 object centre (A): 45.87650 24.08600 15.85850 number of atom coordinates read : 2373 total number of charged atoms : 2231 net assigned charge : 3.500023 assigned positive charge : 362.1461 centred at (gu) : 90.36817 89.12182 89.00556 assigned negative charge : -358.6466 centred at (gu) : 90.40257 88.97796 88.92669 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7608 nv = 96 ne = 84 npr = 47734 no. pairs analyzed = 47734 no. exposed pairs = 2859 no. arc points = 20491 no. surface atoms = 965 nbur = 1408 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 429 mr = 4272 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2700000 number of dielectric boundary points 3714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1912 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8653 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2245227E-08 4.0153754E-08 midg,1,midg; midg,igrid,midg -4.1551967E-08 6.0855179E-08 1,midg,midg; igrid,midg,midg 3.0289808E-08 7.4425608E-09 gauss-seidel spectral radius is 0.9890556 estimated iterations to convergence 78 setup time was (sec) 0.4900000 now iterating at: 14:04:35 rms-change max change #iterations 0.1895761 27.19009 at 10iterations 2.2244891E-02 3.166199 at 20iterations 2.6810511E-03 0.3387032 at 30iterations 3.5622751E-04 4.6073914E-02 at 40iterations 6.1717306E-05 9.4718933E-03 at 50iterations finished qdiffx linear iterations at : 14:04:37 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 6.1717306E-05 9.4718933E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 14:04:38 3.068u 0.147s 0:03.57 89.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 14:04:38 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2373 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.067043 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 21.36800 70.38500 ymin,ymax (A): -1.748000 49.92000 zmin,zma (A): -5.585000 37.30200 x,y,z range (A): 49.01700 51.66800 42.88700 scale (grids/A): 2.067043 object centre (A): 45.87650 24.08600 15.85850 number of atom coordinates read : 2373 total number of charged atoms : 2231 net assigned charge : 3.500023 assigned positive charge : 362.1461 centred at (gu) : 91.10399 87.36495 87.01664 assigned negative charge : -358.6466 centred at (gu) : 91.20737 86.93375 86.77991 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20491 grid for indexing accessible points = 1.400000 m= 30370 mr = 57166 m= 5120 mr = 22765 m= 483 mr = 3321 m= 13 mr = 251 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1556 time to turn everything in is 0.5700000 number of dielectric boundary points 33954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17710 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6890144 object centre at (A) : 45.87650 24.08600 15.85850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6371292E-03 4.1961834E-02 midg,1,midg; midg,igrid,midg -2.6960902E-02 1.7363353E-02 1,midg,midg; igrid,midg,midg 3.9585434E-02 -1.1005501E-02 gauss-seidel spectral radius is 0.9988095 estimated iterations to convergence 229 setup time was (sec) 0.8300000 now iterating at: 14:04:39 rms-change max change #iterations 4.761996 224.4928 at 10iterations 2.334868 82.05128 at 20iterations 1.150968 40.31984 at 30iterations 0.5678893 16.07481 at 40iterations 0.2805223 9.386873 at 50iterations 0.1379231 4.171642 at 60iterations 6.8005353E-02 2.047058 at 70iterations 3.3588041E-02 0.9767227 at 80iterations 1.6633684E-02 0.4815178 at 90iterations 8.1982696E-03 0.2493496 at 100iterations 4.0704254E-03 0.1292725 at 110iterations 2.0240825E-03 6.1719894E-02 at 120iterations finished qdiffx linear iterations at : 14:04:45 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 2.0240825E-03 6.1719894E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 14:04:46 6.959u 0.164s 0:07.48 95.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 14:04:46 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2373 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 3.100565 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 21.36800 70.38500 ymin,ymax (A): -1.748000 49.92000 zmin,zma (A): -5.585000 37.30200 x,y,z range (A): 49.01700 51.66800 42.88700 scale (grids/A): 3.100565 object centre (A): 45.87650 24.08600 15.85850 number of atom coordinates read : 2373 total number of charged atoms : 2231 net assigned charge : 3.500023 assigned positive charge : 362.1461 centred at (gu) : 91.65588 86.04733 85.52465 assigned negative charge : -358.6466 centred at (gu) : 91.81096 85.40048 85.16980 start vw surface at 0.1800000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 187820 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20491 grid for indexing accessible points = 1.400000 m= 97640 mr = 137925 m= 36544 mr = 80758 m= 9527 mr = 29662 m= 1858 mr = 7251 m= 235 mr = 1370 m= 11 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 5055 time to turn everything in is 1.780000 number of dielectric boundary points 76492 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 17848 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.067043 object centre at (A) : 45.87650 24.08600 15.85850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4276519E-02 0.3970592 midg,1,midg; midg,igrid,midg -0.2626058 0.3991673 1,midg,midg; igrid,midg,midg 0.4120501 -0.3938759 gauss-seidel spectral radius is 0.9992918 estimated iterations to convergence 296 setup time was (sec) 2.060000 now iterating at: 14:04:48 rms-change max change #iterations 10.75088 456.3550 at 10iterations 6.330333 148.1575 at 20iterations 3.719769 68.03590 at 30iterations 2.187395 46.37602 at 40iterations 1.284572 25.16253 at 50iterations 0.7514235 13.21226 at 60iterations 0.4399786 9.346019 at 70iterations 0.2570823 4.462395 at 80iterations 0.1504691 2.694378 at 90iterations 8.7952256E-02 1.709473 at 100iterations 5.1304139E-02 0.8675475 at 110iterations 2.9875213E-02 0.5143013 at 120iterations 1.7506480E-02 0.2766514 at 130iterations 1.0216960E-02 0.1793537 at 140iterations 6.0006692E-03 0.1086502 at 150iterations 3.5193306E-03 6.0783386E-02 at 160iterations 2.0820352E-03 3.6870956E-02 at 170iterations 1.2406799E-03 2.3715973E-02 at 180iterations finished qdiffx linear iterations at : 14:04:57 total time elapsed so far: 11.67000 # loops : 180 mean,max change (kT/e) : 1.2406799E-03 2.3715973E-02 energy calculations done at 11.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.85000 DelPhi exited at 14:04:58 11.848u 0.181s 0:12.34 97.4% 0+0k 0+0io 0pf+0w